Need help troubleshooting starting issue

[Arudinne]

So, as a preface I tried searching, but I couldn't find anything directly related to my issue.

My bike is a 2001 GS500E that has been completely rebuilt with a 97 engine (the one it came with was toast) and the rest of the bike is basically GS500F parts. most parts are 2006+

The rotor on the right side has been replaced with the newer version, so I know that's good.

Here is the issue. While I was building it, it was able to start when I was running it without the airbox in my garage, and the exhaust header was not fully sealed (I only had two of the bolts as i lost the other two.

Now it's fully assembled, has an airbox, filter, new exaust gaskets and the exhaust is bolted down with 4 new bolts, and  it turns over, but won't start. The gas has been in the tank for maybe a month tops with some seafoam. The battery died last night, so I'm going to try again tonight.

So far I've tried adjusting the idle screw on the bottom, varying amounts of choke with and without throttle.

I've tried the frame petcock in all 3 positions and the tank petcock is turned on. I should also note, it was able to start with all of these components prior to the final assembly.

Does anyone have any suggestions?

[Arudinne]

So.. after letting the battery charger, the GS fired right up. The idle is a bit high and it still needs some minor adjustments, but in the midst of my testing the bike, after i took it around the block twice, it died as i was rolling down my driveway for a third run, and woudn't turn over.

Some quick research and testing, and I have found that there is a short in one of the stator coils.